M. Lin, J. Wang, Q. Gao, C. Wu, M. Liu and Zh. WangFruit dehiscence is a crucial physiological disorder in fruit crops. Fruit cracking may frequently cause more than 50% of yield losses in Chinese jujube (Ziziphus jujuba Mill.). In this study, we carried out a combined transcriptome sequencing and proteome analysis in Chinese jujube to reveal the molecular mechanisms involved in fruit cracking. A total of 31,272 transcripts and 5,480 proteins were identified. Of these, 5,425 genes were shared at both transcriptome and proteome levels. Compared to non-cracked fruits, 161 differentially expressed genes were revealed in cracked fruits, of which 39 upregulated and 122 downregulated genes. Proteome analysis revealed 182 differentially expressed proteins associated with fruit cracking, of which 68 upregulated and 114 downregulated. Validation of gene expression by realtime quantitative-polymerase chain reaction of 14 selected DEGs were found to regulate cell wall metabolism, unsaturated fatty acid oxidation, plant-pathogen interaction and hormone balance, endoglucanase, pectinesterase, peroxidases, and phytohormone signal transduction genes and calcium-binding protein. The expression levels of POD17, EG12, CML23, ARF, JAZ, AUX/IAA, and SAUR genes were consistent with the transcriptome analysis results. The gene expression levels of POD17 and POD51 were consistent with the proteomics data. However, the expression levels of genes CML23, PE17 and GH3.1 were contradictory with their proteome expression levels. Further analysis of the expression levels of the 14 genes from fruit skins of different samples at various stages of fruit cracking revealed that 11 genes were highly expressed in cracked fruits, suggesting these genes play important roles in fruit cracking. A putative calcium-binding protein CJML19 showed medium-low expression in cracked fruit skins, which may help regulate water entry/exit and may be associated with cracking resistance.